-----Original Message-----
From: Gerard Bricogne [mailto:g...@globalphasing.com]
Sent: 12 January 2009 12:09
To: Ian Tickle
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] structure (factor) amplitude
Dear Ian,
My reply to this question will be less literate and less
democratic
than yours. In spite of the nice Alice quote, I remain in
favour of trying
to use compound names whose internal structure is, as much as
possible,
"isomorphic" to the composition of meanings they refer to
(even though I am
not necessarily an unconditional fanatic of OOP). Even if,
allegedly, only
God has a name for each object that completely specifies it
and even gives
it its very existence, I feel it is not unrealistic nor
immodest to do our
best to achieve this in our scientific language. If we
modelled the rigour
of scientific language on that of Lewis Carroll's, we would
be in serious
trouble (perhaps this is why scientists enjoy his humour so
much: it is
like taking off a pair of tight shoes; and it was probably
his own escape
from the rigours of mathematical logic).
In this case, the word "factor" refers to the fact that,
in the Darwin
formula for an integrated intensity, there are many factors
in a complicated
algebraic expression, and that one of them depends on the
internal structure
of the crystal. The relation to Fourier theory makes it
desirable to use as
the basic structure-dependent quantity the complex Fourier
coefficient of
the electron density, so the latter then becomes known as the
"structure
(-dependent) factor (in the Darwin formula)". Being a complex
number, it
inherits as an attribute the modulus of that complex number,
for which the
synonym "amplitude" is used - regrettably, but possibly
because the word
"modulus" was already widely used, e.g. in the theory of elasticity.
Therefore the expression "structure factor amplitude"
can be parsed as
being "the amplitude (a.k.a. modulus) of a complex number
which is involved
in the structure-dependent factor in the Darwin formula".
Along with Dirk
Kostrewa I vote for retaining the full-length expression, as
the abbreviated
one makes one think that a structure has an amplitude ... .
Abbreviations can be great, but they can also result in
a substantial
loss of intelligibility. Look at the transition to "Brazilian
spelling" in
Portuguese, whereby "optimo" is abbreviated to "otimo". A
non-Portuguese
speaker (even an English-only speaker!) can understand the
word from its
first spelling because the Latin derivation is clear; but
this is no longer
the case for the abbreviated one, unless one also remembers
what it is an
abbreviation of. Similarly, "structure amplitude" does not
tell you that
there is a complex number called the structure factor, of which one
is
considering the amplitude/modulus.
Sorry for this long message: as the question originated
from Bernhard,
who is in the process of writing a textbook, I think it is
important that
points of terminology like this one be given careful
consideration and a
satisfactory conclusion; so I hope that many other people
will give some
attention to this thread (even if they disagree with me!).
With best wishes,
Gerard.
--
On Mon, Jan 12, 2009 at 11:09:34AM -0000, Ian Tickle wrote:
I think there's a confusion here between the name of an
object (what you
call it) and its description (i.e. its properties). The name of the
object is "structure amplitude" and it's description is
"amplitude of
the structure factor", or if you prefer the shortened form
"structure
factor amplitude". This distinction was of course carried
to absurdity
in "Alice through the Looking Glass":
"It's long." said the Knight, "but it's very, very
beautiful. Everybody
that hears me sing it - either it brings tears to their
eyes, or else -"
"Or else what?" said Alice, for the Knight had made a sudden pause.
"Or else it doesn't, you know. The name of the song is
called 'Haddocks'
Eyes.'"
"Oh, that's the name of the song, is it?" Alice said, trying to feel
interested.
"No, you don't understand," the Knight said, looking a little vexed.
"That's what the name is called. The name really is 'The Aged, Aged
Man.'"
"Then I ought to have said 'That's what the song is called'?" Alice
corrected herself.
"No you oughtn't: that's another thing. The song is called 'Ways and
Means' but that's only what it's called, you know!"
"Well, what is the song then?" said Alice, who was by this time
completely bewildered.
"I was coming to that," the Knight said. "The song really
is 'A-sitting
On a Gate': and the tune's my own invention."
Cheers
-- Ian
-----Original Message-----
From: owner-ccp...@jiscmail.ac.uk
[mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of Dirk Kostrewa
Sent: 12 January 2009 10:52
To: CCP4BB
Subject: Re: [ccp4bb] structure (factor) amplitude
... despite these informations, I still prefer "structure factor
amplitude", because it is the amplitude of the "structure
factor" ...
Best regards,
Dirk.
Am 12.01.2009 um 11:42 schrieb Ian Tickle:
I was taught 'structure amplitude' - makes perfect
sense to me! Why
does 'structure amplitude' make any less sense than 'structure
factor'?
It also clearly made sense to Phil Coppens, a
crystallographer of
considerable repute, see ITC Vol. B (2nd Ed.), sect
1.2., p.10: 'The
Structure Factor'. To quote the introduction to the
section: "The
'structure factor' is the central concept in structure
analysis by
diffraction methods. Its modulus is called the 'structure
amplitude'".
Also I did a 'Google vote' for the two terms. 'Structure
amplitude'
has
11300 hits. 'Structure factor amplitude' has only
4750. So all
round I
would say that 'structure amplitude' wins by a
considerable margin.
Cheers
-- Ian
-----Original Message-----
From: owner-ccp...@jiscmail.ac.uk
[mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of Pavel Afonine
Sent: 11 January 2009 03:01
To: Ethan A Merritt
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] structure (factor) amplitude
On 1/10/2009 5:14 PM, Ethan A Merritt wrote:
On Saturday 10 January 2009, Bernhard Rupp wrote:
Dear All,
I am getting conflicting comments on the use of
'structure factor amplitude'
vs. just
'structure amplitude'
for |F|.
???
That's just... odd.
|F| is the amplitude of F.
But no way F is a "structure".
I agree. If F is a structure factor then |F| is a structure
factor amplitude. "structure amplitude" doesn't make
much sense...
Pavel.
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Astex Therapeutics Ltd monitors, controls and protects all
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policy. The Company accepts no liability or responsibility
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should check this email and any attachments for the presence
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email. E-mail is susceptible to data corruption,
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